User Profile: bonesiii

bonesiii

Member Since: October 14, 2012

Comments

123 To page: Go
  • [-2] July 22, 2014 at 4:59pm

    Nice! And they did it quick too. Maybe another old-earther argument bites the… er… sand?

  • July 22, 2014 at 2:41pm

    Alright, got time for one more ICR source:

    http://www.icr.org/article/ongoing-telomere-research-at-odds-with/

    “The genome-wide presence of internal telomere sequences is not well documented in the scientific literature. In our research, it became evident that telomere repeats were not unique to the ends of chromosomes.”

    That’s basically covered by previous quotes, but notice that this appears to (mostly) confirm that they did indeed neglect the falsification work.

    “chromosome 2 (the supposed fusion product) contains over 91,000 (0.23 percent) intact internal telomere sequences. Fewer than 300 of these can be attributed to the so-called fusion site.”

    “In the fusion site on chromosome 2, there are a small number of cases where the 6-base telomeres occur in perfect tandem, but never more than two in a row. However, other internal regions of chromosome 2 contain perfect tandems of three to ten telomere repeats.”

    This seems to lead to the odd necessity (under evolution), based on your premises earlier, that these are the remnants of much older fusions, but actually degenerated less, even though they weren’t in a usually disabled region near the centromere! More likely something else is going on here, apparently.

  • July 22, 2014 at 2:10pm

    For example, the original article I cited admitted:

    “Although far from being beyond doubt, a good case can be made that humans did, indeed, have 24 chromosome pairs originally”

    It would be much easier for them to just hide this and claim fusion definitely didn’t happen, but CMI holds to much higher standards than that. I’ve seen many other examples across various articles. Obviously, evolutionist sources need consulted too, though. But that’s where systematic uncertainty comes in — we are unafraid to learn everything, since we just want the truth, while evolutionists seem to like to stay in ignorance and seek out only one side. (Besides, there would be little point to CMI ignoring sound points by evolutionists, if any, simply out of bias; they can’t censor the rest of the ‘net, yanno.)

  • July 22, 2014 at 1:51pm

    “you would have easily been able to answer the question you raised — whether the match ups are based on very fragmentary evidence”

    That actually WAS answered already with a resounding yes. There are more quotes to this end in the second JoC article too that I didn’t bother to include here. Like it or not, they were fragmentary, as was the entire chimp genome project, by the way (and the estimate of total similarity went down, keep in mind).

    “you can’t consider all possibilities by getting the lions share of your information from a single apologist site.”

    That is actually exactly my point to you, fom! You are ignoring creationist sources and getting all your claims from evolutionist sites! You need to have ALL-INCLUSIVE research before you can make confident “one way is definite” claims as you have been doing. It is appropriate, then, to force you to see the things you’ve been purposefully ignoring. Until you know absolutely everything, you should remain in uncertainty as I’ve been doing, and seek more knowledge from both sides. :)

    Besides, this one apologist site has a stellar track record of being honest when research so far seems (key word) to support evolutionist positions. There are several more quotes like that at the pages I’ve been directing to you that I also didn’t put up here. You can check it out for yourself. :)

  • July 22, 2014 at 1:50pm

    “you are wrong. the match is based on the whole of the chromosomes in question.”

    Well aware, fom. But it was based on fragmentary evidence, and it seems closer examination with more advanced techniques has been neglected. And this was covered earlier by this quote (I’ll expand it a bit this time):

    “1) Synteny exists, but this is not a surprise.

    a) Genomic information appears modular and so the stuff coded by the chimpanzee chromosomes would be expected to be found somewhere. Where else would we expect it to be found if all the other genomic regions are already accounted for?”

    In other words, some similar sequences between similar beings (like chimps and humans) would be expected under both models. You could work a loose match between many different chromosomes, and we would expect one to be the closest match. And since sites that could be confused for fusion sites appear to be common anyways, you should probably find at least one on the closest match chromosome. This is fully consistent, it appears, with a non-fusion biblical model, given all the other details mentioned so far. Again, I’m not personally going to go as far as Thompkins did and say fusion is definitely ruled out (though obviously he would know better than me lol), but a strong case doesn’t seem to exist, and certainly not one that requires your molecular clock assumption.

  • July 22, 2014 at 1:36pm

    “The alleged fusion sequence contained a different signature, a telomere-telomere fusion, and, if real, would be the first documented case ever seen in nature.”

    http://www.icr.org/article/new-research-debunks-human-chromosome/

    Interestingly, in this one he claims to have “fully debunked” the fusion model. He says this region is part of a DDX11L2 gene which is indeed regulatory. I don’t know that evolutionists would agree that this debunks it, but it does seem to me there’s very little real evidence for a fusion there.

    Worth mentioning this quote from the comments section of the second JoC article:

    “One reason they [evolutionists] have not come up with these results is that they have not thought to look. I have published several articles in evolutionary journals highlighting things that should have been obvious to all, but nobody else saw them.

    Another reason is that they do not necessarily want contrary data published that contradicts the status quo. Human psychology is a difficult thing to deal with in the sciences, but it is also a powerful force.

    Are they hiding something? I don’t believe so, but the power of a paradigm often blinds people to the obvious – for a time.”

    We see this often with evolutionists, where, for whatever motives, they seek positive evidence, but fail to do the falsification work, and leap right to using it as a strong argument for evolution. Human nature, I guess.

  • July 22, 2014 at 1:33pm

    “Identity values ranged from 80.5 to 100%, supporting the conclusion that the telomere fusion site core sequence is not unique to its pericentric location on chromosome 2, and instead represents a sequence feature (motif) scattered throughout the human genome.”

    This supports one of the earlier possibilities I mentioned — that the evolutionists may have fooled themselves into thinking they had a successful prediction at that one site only because sites like this are common and they just didn’t look anywhere else.

    “Interestingly, human chromosomes 2, 16, 21 and 22 were peppered with the ‘fusion site’ sequence over the length of their entire euchromatic landscape”

    “When the 798-bp core fusion sequence was BLASTN queried against the chimpanzee genome, the significantly placed hit count was reduced to 19, only 22% of the amount observed in the human genome.”

    ICR’s many articles on the subjects should be consulted too before you go claiming things definitely. I know less about that, admittedly, but a search just now turned up this, also by Thompkins:

    “this new fusion-like sequence wasn’t what the researchers were expecting to find since it contained a signature never seen before. All known fusions in living animals are associated with a sequence called satellite DNA (satDNA) that fuses in one of the two following scenarios: 1) satDNA-satDNA or 2) satDNA-telomereDNA.” [more in next]

  • July 22, 2014 at 1:32pm

    “These numbers are roughly equal, indicating that both the forward and reverse orientation of the telomere motif occurs quite frequently at internal sites across the length of chromosome 2.”

    So again, it seems the telomeres don’t really need special explaining. And again, if this was already the case in the two chromosomes in a biblical fusion model, and a fusion did occur, the actual end-cap telomeres could be much shorter than Miller, etc. are assuming, so even with a simple fusion, the other genes found around the actual fusion site could be original to the pre-fusion genome (for the most part; some degeneration would presumably happen in the biblical model too).

    “A more valid explanation for the telomere-like features present at the putative fusion site is that they may represent some form of a distinct genomic motif. To test this idea, a 798-bp fragment (figure 2) encompassing the fusion site and the region where the telomeric motifs are more densely populated was used as a query subject in a BLAT17 search on the most recent build of the human genome (v 37.1; http://www.genome.usc.edu) with masking disabled. The results revealed a total of 159 significantly placed hits throughout the genome on human chromosomes 1–11, 15, 18–20, X and Y. The homologous regions for these hits included areas near telomeres, pericentric areas, and a wide variety of internal euchromatic sites. [cont. in next]“

  • July 22, 2014 at 1:31pm

    “Even while completely disregarding a consensus 6-base reading frame when iterating through the repeats, for the left (plus strand) side of the fusion site, there are only 34 intact TTAGGG motifs (table 1). This analysis uses a generous allowance of 92,690 bases to the left of the fusion site where the first TTAGGG repeat is found on BAC RP11-395L14, well beyond the size of any normal human telomere. Based on the predicted model, thousands of intact TTAGGG motifs in tandem should exist. This is true even if allowing for an extremely high rate of degeneracy, which is an unreasonable expectation because meiotic recombination is suppressed in pericentric DNA due to its close proximity to the centromere.”

    It goes on to describe a similar “paucity” for the right side, though not as low.

    “A complete scan of the 237+ million bases of the assembled euchromatic sequence of chromosome 2 using the Skittle Genome Viewer software package showed that the entire landscape, from end to end, is populated with TTAGGG and CCCTAA motifs. Small, isolated dense clusters of telomere motifs occurred in at least 5 internal locations (data not shown). A complete iteration of the entire plus strand sequence of chromosome 2 (Per script written by Tomkins) indicated a total number of ‘TTAGGG’ and ‘CCCTAA’ occurences at 45,450 and 45,770, respectively (table 2). [quote continued in next]“

  • July 22, 2014 at 1:29pm

    Just found this in one of the related links I actually hadn’t read yet:

    “ROBs have been shown to be non-random and appear to have distinct mechanisms governing their formation.”

    http://creation.com/changing-chromosome-numbers

    That seems to support the possibility I had mentioned of a coded fusion. (If indeed there is any sound evidence for one here versus cherrypicking of slight similarities to one that would be found anyways.)

    Anyways, to the second JoC article now:

    ” The data actually suggest that the core ~800 bp region containing the fusion site is not a unique cryptic and degenerate head-to-head fusion of telomeres, but a distinct motif that is represented throughout the human genome with no orthologous counterpart in the chimpanzee genome on either chromosome 2A or 2B. The DNA sequence evidence for a purported inactivated cryptic centromere site on chromosome 2, supposedly composed of centromeric alphoid repeats, is even more ambiguous and untenable than the case for a fusion site.”

    “While the chromosome 2 fusion model has been routinely discussed in reviews of human evolution, very little new supporting genomic data, although readily available for analysis, has been forthcoming. For the purpose of propagating the dogma surrounding human evolution, several science authors have recently published novice-level science books promoting the hypothetical chromosome 2 model.10,11″

    Footnote 11 references Miller’s book.

  • July 22, 2014 at 5:25am

    “‘So actually, not only is there the possibly of step mutations being fatal as I suggested earlier, apparently the fusion event itself should be fatal!’

    tell that to the men and women who occasionally are born with fused chromosomes, who also manage to not only live, but also reproduce.”

    Nice taking me out of context… rather pointless since anybody can just re-read it, but in case they don’t wanna look for it, the very next sentence said:

    “So, there’s actually other mutations that would (if I’m reading this right) be needed first to turn off those programs before the fusion event.”

    I was also planning to mention a case of this in animals, but figured long posts were long. Guess I should have to cut your counter off at the pass. Whatevs. (I was going to point out that this may — may — be more evidence of a fusion contingency program, which would open the door to any number of transpositions and insertions and the like to explain all the finds mentioned so far and much more besides, all without that mutation clock argument being the only option.)

    “i am beginning to understand why you like creation.com. you, too, tend to speculate in ways that fit your world view, without bothering to check to see if your speculation raises any problems.”

    fom, part of my “truthseeking method” is to consider all possibilities. And you don’t seem to be grasping the difference between sound analysis and “speculation.”

  • July 22, 2014 at 5:22am

    Alright, one last, to that post you got in before my latest, but I’ll have no more time for now for more:

    “‘I’m starting to wonder if the particular chromosome being looked at even matches up to those particular two in chimps at all.’

    of course it does! do you need pictures? thats actually the strongest evidence for the fusion.”

    Quotes I’ve included already seem to cover this. These claimed matchups are apparently based on very fragmentary evidence, not the total genes, so many parts were apparently not considered yet. Also relevant:

    “Genomic information appears modular and so the stuff coded by the chimpanzee chromosomes would be expected to be found somewhere. Where else would we expect it to be found if all the other genomic regions are already accounted for?”

    Being modular means we would expect to find some matchup in a lot of places, so if you go to one place looking for a matchup (a loose one), you might be able to find it just about anywhere, and fool yourself into thinking your prediction was successful. Has it been checked against the entire genome yet to rule this out? It seems not from previous reports I’ve seen.

    “that and the fact that it appears in other early humans like denisovans and neanderthal, as predicted.”

    That would also be predicted under the creation model, so what’s your point?

  • July 22, 2014 at 4:53am

    “creation.com cannot simultaneously assume in its argument both a fusion and thousands of years”

    Quibbling about “assume” aside, yes they can (hold to both, although they don’t necessarily think a fusion is definite). You’re arguing backwards here, based on unknowns — you don’t know that your interpretation is impossible, so you assume it’s the only way, and then say that this means the possibility here must be ruled out. That’s not how logic works, fom. You have to actually rule out ALL other possibilities FIRST (with sound reasoning) before you can say yours is the only way. I covered this earlier with the circular reasoning part. Maybe it wasn’t clear enough, I dunno, but hope this helps. :)

    Clarification from previous post: “is simply genes between the original endcaps”

  • July 22, 2014 at 4:51am

    “‘this assumes that that is actually corruption (mutations over a long period), rather than remnants of information on the originally separate chromosomes that are preserved in the fusion’

    no, bonesiii, because you have to account for the telomeres.”

    Any number of answers given already would seem to do that. :) Especially programmed fusion. But for this to even be relevant, you would first have to establish how common telomeres are throughout genomes. This quote made me wonder about that:

    “both the forward and reverse complement of the telomere motif populate both sides of the fusion site.”

    Which certainly does not sound like a straightforward head to head fusion at all. That makes it seem like telomeres in both directions exist throughout genes (perhaps in sections that regulate the normal telomere endcaps?), and they happen to have only been found at this site because evolutionists were cherrypicking some there to support their fusion model. But what if most of those are native to non-endcap regions, and the supposed “corruption” is simply genes inside the original endcaps, sprinkled with occasional telomere sequences for whatever reasons?

    And all of this ignores the problem of direction of change mentioned in that comment in the original article I linked to from Peter B. — loss of existing genes might make sense under a rate of mutation argument, but gain of many functional genes does not match observations.

  • July 22, 2014 at 4:46am

    I’ve commented before in more detail on why, and a little to the discussion chain immediately below this one. Suffice to say, I put them to the test of the truthseeking method, as a logician, and they pass it generally, while promoters of other worldviews like evolution fail it consistently. I must wonder, given the horrible track record of evolutionists, why do YOU trust THEM? We can all think of a long chain of failed predictions, and any that do work overlap biblical predictions anyways as I’ve cited often in past discussions. By contrast, creationist predictions (like conservative ones lol) tend (to put it mildly) to bear out time and time again.

    “you don’t seem to even read them, but you expect us to.”

    If I hadn’t read the article I linked, why would I be linking it? ;) I’m recommending answers that address arguments being raised. You can’t do that without knowing what’s in them… But see above. (What I didn’t know was what was in your head, anyways, since you didn’t speak clearly! You know, sometimes I wish evolutionists would avoid the traps I include, just for some variety lol…)

    “and even when someone like myself shows you the obvious flaws in their reasoning”

    Such as? You haven’t done this even once yet. You just keep reciting the position they are refuting in various wordings and throwing insults around, and apparently ignoring my answers (like about the mutation rates thing being circular reasoning).

  • July 22, 2014 at 4:40am

    “‘Do you mean the last part (after the colon) here to be the same assumption’? Where did creation.com state this?’

    oh dear, bonesiii, do you not read these sources you provide?

    from creation.com:

    ‘Although far from being beyond doubt, a good case can be made that humans did, indeed, have 24 chromosome pairs originally, and that chromosome fusion has occurred, resulting in our now having only 23. For the sake of the argument, let us concede that this is true.’”

    Lol, that’s what you meant by “assuming”? It clearly says “for the sake of argument.” That’s not at all the same as the assumptions I was talking about which are being used to claim a definite answer. As for reading, like I said, it’s been a while, and I can’t be expected to remember everything perfectly without review (but of course, I expected you to go for that insult… I cued you for it to demonstrate that evolutionists like you just can’t resist any slight hope of sounding superior illogically…).

    And I was asking which assumption you personally meant, since you didn’t specify. But no, I never would have noticed this as being what you meant, since it’s obviously not at all the same kind of assuming I was talking about! (Leave it to evolutionists to invent equivocation fallacy uses I wouldn’t have even thought of, sigh.)

    “why do you trust these guys?”

    If you would read them for at least a year as I often challenge skeptics to do, you’d probably know. [...]

  • July 22, 2014 at 3:51am

    It seems to me that the only clear evidence is the number of chromosomes themselves (ours being two less than chimps as opposed to four or eight, or twenty more, etc.). I’m starting to wonder if the particular chromosome being looked at even matches up to those particular two in chimps at all. Or did they just pick one of similar length (to what the total would be) and cherrypick its contents to paint a false image of a fusion? If so, it’s possible others could fit the data almost as closely (depending on variability in lengths I guess, which I dunno about offhand, but then various types of mutation could explain even that away).

    And as for the similar chromosome number, my guess is that under a non-fusion model, that could be easily explained as simply part of why chimps are so similar to us. I’ve often said it’s silly to act like it’s surprising that their DNA (supposedly) was very similar, since DNA makes them what we see, and we already see that they ARE similar. (However, recently the initial very high estimates of close DNA similarity have been downgraded.) Chromosome number could be part of that.

    Well, that’s as far as I have time for, but that’s hopefully enough to show that the evolutionists’ case is not strong!

    In any event. People walking on all fours…

    *sees that you replied already* Right… I dunno if I’ll have time to get to those right now… reading real quick…

  • July 22, 2014 at 3:50am

    In other words, we need multiple mutations to happen at once.

    “Evolutionists explain the lack of a clearly distinguishable non-functional secondary centromere by arguing that two centromeres would result in major instability when chromosomes pair up during cell division and consequently would be rapidly selected against. According to the evolutionary model, selection would continue until the second centromere was completely non-functional.”

    The article doesn’t, at least here, go into this, so I must wonder — if it is selected against, does that mean cell death and therefore no fusion propogation? But notice this also suggests functionality of the centromere may be controlled in multiple locations, opening up a possibility of even more simultaneous or nearly so mutations being needed.

    “However, the evidence for a second remnant centromere at any stage of sequence degeneracy is negligible. [Continues to describe the alphoid sequence in centromeres, and Fairbanks' claim that one is present at the right site for a disabled centromere.] The main problem with Fairbank’s claim is that alpha-satellite DNA or alphoid DNA, although found in centromeric areas, is not unique to centromeres and is also highly variable. Because highly variable alphoid DNA is also commonly found in non-centromeric regions of human chromosomes, their presence does not indicate the remnants of a degenerate centromere.”

  • July 22, 2014 at 3:49am

    Which personally makes me wonder — if indeed a fusion did happen, isn’t a directed process causing it more likely than something accidental? Although this argument doesn’t seem to preclude the possibility of two telomere ends simultaneously mutating to something that can bond — no idea if that’s possible though. But contingency programmed fusion would explain all of this so far…

    “In the case of an aberrant fusion, a senescence response or programmed cell death (apoptosis) cascade is normally triggered, effectively eliminating the damaged cell from the system.”

    So actually, not only is there the possibly of step mutations being fatal as I suggested earlier, apparently the fusion event itself should be fatal! So, there’s actually other mutations that would (if I’m reading this right) be needed first to turn off those programs before the fusion event.

    “Yet another major problem with the fusion model is the lack of evidence for a cryptic second centromere site. Immediately following the supposed head-to-head telomere fusion, there would have existed two centromeres in the newly-formed chimeric chromosome, one from each of the two fused chromosomes. This type of event had to occur in a cell lineage of the germ-line to be heritable, and one of the centromeres would have had to be immediately eliminated or at least functionally silenced for cell division to progress normally.”

  • July 22, 2014 at 3:46am

    This discussion got me curious so I decided to review those other linked articles about the fusion theory, and post some pull quotes. I don’t have a lot of time, so I probably won’t get all the way through them, but just the early ones should shed some light on the subject.

    “a glaring paucity of telomeric repeats exist that appear mostly as independent monomers, not tandem repeats. Based on the predicted model, thousands of intact motifs in tandem should exist.”

    “both the forward and reverse complement of the telomere motif populate both sides of the fusion site.”

    (!)

    “If a fusion occurred, the alleged sequence no longer resembles telomeric repeats, a problem explained away by fusion supporters by claiming the telomeric repeat area is incredibly degenerate.”

    “The only evolutionary research group to seriously analyze the actual fusion site DNA sequence data in detail were confounded by the results which showed a lack of evidence for fusion”

    “Another problem for the fusion theory is the presence of a wide variety of genes throughout the fusion region.”

    “If the telomere motifs that populate internal areas of chromosomes serve some important, yet unknown function, the chromosome fusion model actually impedes research aimed at determining possible function in these regions.”

    “Assuming that two telomeres exist in a head-to-head fusion produces another major problem, namely that telomeres are designed to prevent fusion.”

123 To page: Go